User:Ty M. Thomson: Difference between revisions
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#Build a model of the pheromone response pathway | #Build a model of the pheromone response pathway | ||
#*Develop a model of the pheromone response pathway that can be used in conjunction with time-dependent stimulation and analysis of the pathway to propose and test hypotheses. Once completed, this model can be used as a predictive tool for pathway response. | #*Develop a model of the pheromone response pathway that can be used in conjunction with time-dependent stimulation and analysis of the pathway to propose and test hypotheses. Once completed, this model can be used as a predictive tool for pathway response. | ||
#**This model is largely already built (with instanced in Matlab and Moleculizer. | #**This model is largely already built (with instanced in Matlab and Moleculizer( [Image:NatBiotech(21)131.pdf]). | ||
#Build a microfluidic device for time-dependent stimulation of cells | #Build a microfluidic device for time-dependent stimulation of cells | ||
#*Design, build and characterize a device to allow for rapid variation of extracellular conditions for cells fixed in a microfluidic channel. | #*Design, build and characterize a device to allow for rapid variation of extracellular conditions for cells fixed in a microfluidic channel. |
Revision as of 14:12, 12 May 2005
Thesis Topic
The main objectives of my work is to develop the tools to perform time-dependent stimulation and analysis of signaling pathways, and show that this is more powerful than traditional time-independent or step response analysis. I am using a computational model of the prototype system, the yeast pheromone response pathway, to generate hypotheses about the pathway. In order to test these hypotheses, time-dependent stimuli will be delivered to cells via a microfluidic device, and in vivo fluorescent reporters will be used to observe the system state. In addition to showing the strengths of this new approach to studying biological systems, I would like to use it to further our understanding of the pheromone response pathway.
Research Goals
My research can be broken down into 4 main goals (that follow for the most part chronologically).
- Build a model of the pheromone response pathway
- Develop a model of the pheromone response pathway that can be used in conjunction with time-dependent stimulation and analysis of the pathway to propose and test hypotheses. Once completed, this model can be used as a predictive tool for pathway response.
- This model is largely already built (with instanced in Matlab and Moleculizer( [Image:NatBiotech(21)131.pdf]).
- Develop a model of the pheromone response pathway that can be used in conjunction with time-dependent stimulation and analysis of the pathway to propose and test hypotheses. Once completed, this model can be used as a predictive tool for pathway response.
- Build a microfluidic device for time-dependent stimulation of cells
- Design, build and characterize a device to allow for rapid variation of extracellular conditions for cells fixed in a microfluidic channel.
- Investigate the pathway with time-dependent stimulation
- Examine the frequency filtering characteristics of the pheromone response pathway in order to study the limits of propagation of time-varying signals through the pathway. Use the model to form and test hypotheses generated by studying the response of the pathway to time-dependent stimulation.
- Identify and apply techniques for non-linear system identification
- Identify and apply tools developed for other fields to the analysis of signaling pathways, particularly with respect to time-dependent stimulation.